I would try to bleach a small section of the stains to see what happens.

If you use super glue, get a liquid type that is specifically meant for use on wood. Some formulations don't work as well on wood. Woodcraft sell several types.

Get this kit so you can inject the glue in the pocket. You might need to use a sharp knife to slice into through the lifted ply so you can get the glue in there. Once clamped and sanded the slice should disapear.

http://www.highlandwoodworking.com/cagluedispensepak.aspx

use some wax paper over the repair area when you clamp it to prevent the clamp from getting glued to the shell.

Just thought I'd throw my 2c in regarding staining this drum. I recently stripped an 80's Yamaha set, which was originally lacquered. See the picture below for a great large-pad sanding tool, made by Grizzly. After spending many hours sanding these drums very smooth, my stain simply would not take to the wood. It sort of sat on top and looked horrible. The trouble may have been related to previous lacquer or the birch shells. In either event, I was surprised that what appeared to be bare wood still held enough of the original finish to block the new stain. Your glue residue/mold may produce the same result. I ended up wrapping mine with wood veneer, then staining.

Best of luck. Love the drum.

Thanks for the input, that is one of my concerns as well. However, I'm a bit confused, I've read a couple posts here where people mention sanding down to a very fine, smooth surface before staining, yet I have read elsewhere that the shell should not be sanded down so finely, only sand to 100 - 120 or so grit so the wood takes the stain better.

Well, it's been a couple of days since I have been able to check in here, but a couple things have come up -

1) It is hard to take a picture that shows the extent of the delamination. The larger pockets are 2-3" wide. I have been able to get enough glue far enough down to get the top ply to re bond with the shell. Is it a good idea to gently split these pockets open so I can get more glue inside, then clamp it? Some areas have no split to begin with, so there is no way of getting glue in there unless I cut it open with a razor.

2) I'm concerned that staining the shell may not be a viable option. If I try to re-cover the drum, will the delamination cause the wrap to not sit flat?